__compareDateSite__ (
        self,
        first,
        second,
        )

__compareDateSite__ is a private method to help sort by start date and then site.

first, second - lists of experiment information as parsed from expTab.txt filesself.__expStartDateCol

__getPositionByExpIdBinarySearch__ ( self,  expId )

__getPositionByExpIdBinarySearch__ is a private method that does a binary search for a given experiment id.

May fail if experiment ids are not in order, or if expId does not exist. If fails, returns None.

Input: expId - experiment ID (int) to search for

Returns: position (int) of expId. First position = 0. Returns None if not found.

__init__ (
        self,
        madDB=None,
        initFile=None,
        )

__init__ initializes MadrigalExperiment by reading from expTab.txt (or initFile).

Inputs: Existing MadrigalDB object, by default = None.

String representing the full path to the metadata file. Default is None, in which case file read is MadrigalDB.getMetadataDir()/expTab.txt.

Returns: void

Affects: Initializes all the class member variables.

Exceptions: MadrigalError thrown by MadrigalMetadata if file not opened or parsed successfully.

__str__ ( self )

return possibly modified file as a string in same format as writeMetadata

getExpCount ( self )

getExpCount returns number of experiments in MadrigalExperiment object

getExpDirByExpId ( self,  expId )

getExpDirByExpId returns the full experiment directory for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the full experiment directory (string). Returns None if experiment id not found. Uses experiment url to determine directory.

Affects: None

Exceptions: None

getExpDirByPosition ( self,  position=0 )

getExpDirByPosition returns the full experiment directory of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the full experiment directory, or None if position >= number of experiments. Uses experiment url to determine directory.

Affects: None

Exceptions: None

getExpEndDateTimeByExpId ( self,  expId )

getExpEndDateTimeByExpId returns the ending date/time of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the experiment end date/time in the standard python form of 9 item tuple in UTC. Returns None if experiment id not found. Since mktime does not go before 1970, I use date.c methods, and miss only day of week and DST flag

Affects: None

Exceptions: None

getExpEndDateTimeByPosition ( self,  position=0 )

getExpEndDateTimeByPosition returns the ending date/time of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment end date/time in the standard python form of 9 item tuple in UTC. Returns None if position >= number of experiments. Since mktime does not go before 1970, I use date.c methods, and miss only day of week and DST flag

Affects: None

Exceptions: None

getExpIdByPosition ( self,  position=0 )

getExpIdByPosition returns the experiment id of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment id (integer), or None if position >= number of experiments.

Affects: None

Exceptions: MadrigalError if any item in row cannot be cast to correct format

getExpLinksByExpId ( self,  expId )

getExpLinksByExpId returns a list of (title, url) tuples containing all links for this experiment.

Inputs:

Inputs: Experiment Id (integer).

Returns: a list of (title, url) tuples containing all links for this experiment.

In order to be a link, a file must be in the experiment directory in the form *.html, */index.html, or */*/index.html. The title is parsed from the title in the head; if not found, returns No title as title. The follow file extensions are also links if found in the main experiment directory: ['ps', eps, png, jpg, jpeg, pdf, 'gif']. For these files, the title is simply the basename.

Affects: None

Exceptions: None

getExpNameByExpId ( self,  expId )

getExpNameByExpId returns the experiment name for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the experiment name (string). Returns None if experiment id not found.

Affects: None

Exceptions: None

getExpNameByPosition ( self,  position=0 )

getExpNameByPosition returns the experiment name of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment name, or None if position >= number of experiments.

Affects: None

Exceptions: None

getExpSiteIdByExpId ( self,  expId )

getExpSiteIdByExpId returns the site id (int) for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the site id for this experiment. Returns None if experiment id not found.

Affects: None

Exceptions: None

getExpSiteIdByPosition ( self,  position=0 )

getExpSiteIdByPosition returns the experiment site id of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment site id (integer), or None if position >= number of experiments.

Affects: None

Exceptions: MadrigalError if any item in row cannot be cast to correct format

getExpStartDateTimeByExpId ( self,  expId )

getExpStartDateTimeByExpId returns the starting date/time of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the experiment start date/time in the standard python form of 9 item tuple in UTC. Returns None if experiment id not found. Since mktime does not go before 1970, I use date.c methods, and miss only day of week and DST flag

Affects: None

Exceptions: None

getExpStartDateTimeByPosition ( self,  position=0 )

getExpStartDateTimeByPosition returns the starting date/time of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment start date/time in the standard python form of 9 item tuple in UTC. Returns None if position >= number of experiments. Since mktime does not go before 1970, I use date.c methods, and miss only day of week and DST flag

Affects: None

Exceptions: None

getExpUrlByExpId ( self,  expId )

getExpUrlByExpId returns the experiment url for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the experiment url (string). Returns None if experiment id not found.

Affects: None

Exceptions: None

getExpUrlByPosition ( self,  position=0 )

getExpUrlByPosition returns the experiment url of the experiment at given position.

Inputs: position of experiment in list (first position is zero). Defaults to first.

Returns: the experiment url, or None if position >= number of experiments.

Affects: None

Exceptions: None

getKinstByExpId ( self,  expId )

getKinstByExpId returns the kinst (integer) of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the experiment kinst (integer). Returns None if experiment id not found.

Affects: None

Exceptions: None

getKinstByPosition ( self,  position=0 )

getKinstByPosition returns the kinst (kind of instrument code) of the experiment at given position.

Inputs: position of file in list (first position is zero). Defaults to first.

Returns: the kindat (kind of data code) of the file at given position as an integer. Returns None if position >= number of files.

Affects: None

Exceptions: Thrown if kindat column cannot be parsed into an integer

getLine ( self,  position )

getLine returns the line at a given position. Returns None if position > number of lines.

Inputs: position - position in file. First line = 0

getPIByExpId ( self,  expId )

getPIByExpId returns the principal investigator (string) of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the principal investigator's name (string). Returns None if experiment id not found. Since not all expTab.txt files may have this column, returns None if the column does not exist.

Affects: None

Exceptions: None

This method added in Madrigal 2.6

getPIByPosition ( self,  position=0 )

getPIByPosition returns the principal investigator of the experiment at given position.

Inputs: position of file in list (first position is zero). Defaults to first.

Returns: the principal investigator's name (string) of the file at given position as a string. Returns None if position >= number of files. Since not all expTab.txt files may have this column, returns None if the column does not exist.

Affects: None

Exceptions: None

This method added in Madrigal 2.6

getPIEmailByExpId ( self,  expId )

getPIEmailByExpId returns the principal investigator email (string) of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the principal investigator's email (string). Returns None if experiment id not found. Since not all expTab.txt files may have this column, returns None if the column does not exist.

Affects: None

Exceptions: None

This method added in Madrigal 2.6

getPIEmailByPosition ( self,  position=0 )

getPIEmailByPosition returns the principal investigator email of the experiment at given position.

Inputs: position of file in list (first position is zero). Defaults to first.

Returns: the principal investigator's email (string) of the file at given position as a string. Returns None if position >= number of files. Since not all expTab.txt files may have this column, returns None if the column does not exist.

Affects: None

Exceptions: None

This method added in Madrigal 2.6

getSecurityByExpId ( self,  expId )

getSecurityByExpId returns the security code (integer) of the experiment for a given experiment id.

Inputs: Experiment Id (integer).

Returns: the security code (integer). Returns None if experiment id not found.

Affects: None

Exceptions: None

getSecurityByPosition ( self,  position=0 )

getSecurityByPosition returns the security code of the experiment at given position.

Inputs: position of file in list (first position is zero). Defaults to first.

Returns: the security code (integer) of the file at given position as an integer. Returns None if position >= number of files.

Affects: None

Exceptions: Thrown if security column cannot be parsed into an integer

setExpEndDateTimeByPosition (
        self,
        endDateTime,
        position=0,
        )

setExpEndDateTimeByPosition sets a new MadrigalExperiment end date and time by position.

Inputs:

endDateTime - a python datetime object to set the exp end date and time to.

position - which experiment row to change - defaults to 0

Returns: None.

Affects: sets exp end date and time in self.__fileList.

Exceptions: None

setExpIdByPosition (
        self,
        position,
        expId,
        )

setExpIdByPosition sets the experiment id of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

expId - the new experiment id to use

Returns: None.

Affects: sets the experiment id of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

setExpKinstByPosition (
        self,
        position,
        expKinst,
        )

setExpKinstByPosition sets the experiment kinst of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

expKinst - the new experiment kinst to use

Returns: None.

Affects: sets the experiment kinst of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

setExpNameByPosition (
        self,
        position,
        expName,
        )

setExpNameByPosition sets the experiment name of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

expName - the new experiment name to use

Returns: None.

Affects: sets the experiment name of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

setExpSiteIdByPosition (
        self,
        position,
        expSiteId,
        )

setExpSiteIdByPosition sets the experiment site id of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

expSiteId - the new experiment site id to use

Returns: None.

Affects: sets the experiment site id of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

setExpStartDateTimeByPosition (
        self,
        startDateTime,
        position=0,
        )

setExpStartDateTimeByPosition sets a new MadrigalExperiment start date and time by position.

Inputs:

startDateTime - a python datetime object to set the exp start date and time to.

position - which experiment row to change - defaults to 0

Returns: None.

Affects: sets exp start date and time in self.__fileList.

Exceptions: None

setExpUrlByPosition (
        self,
        position,
        expUrl,
        )

setExpUrlByPosition sets the experiment url of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

expUrl - the new experiment url to use

Returns: None.

Affects: sets the experiment url of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

setPIByPosition (
        self,
        position,
        PI,
        )

setPIByPosition sets the principal investigator (string) of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

PI - the new experiment principal investigator's name (string) to use

Returns: None.

Affects: sets the principal investigator of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

This method added in Madrigal 2.6

setPIEmailByPosition (
        self,
        position,
        PIEmail,
        )

setPIEmailByPosition sets the principal investigator email (string) of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

PIEmail - the new experiment principal investigator's email (string) to use

Returns: None.

Affects: sets the principal investigator email of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

This method added in Madrigal 2.6

setSecurityByPosition (
        self,
        position,
        securityCode,
        )

setSecurityByPosition sets the security code (integer) of the experiment at given position.

Inputs:

position - position of experiment in list (first position is zero).

securityCode - the new experiment security code (integer) to use

Returns: None.

Affects: sets the security code of the experiment at given position

Exceptions: MadrigalError if any item in row cannot be cast to correct format, or position not found.

sortByDateSite ( self )

sortByDateSite will resort self.__fileList so that experiments are listed first by experiment start date, and then by site

writeMetadata ( self,  newFullPath=None )

writeMetadata writes a new version of the expTab.txt file.

Inputs: newFullPath: a new path to write the expTab.txt file to, if not the same as the original metadata file opened. Defaults to None, which overwrites metadata file that was read from.

Returns: None.

Affects: Writes updated version of metadata file.

Exceptions: If unable to write file